Author: tlinnet
Date: Wed Apr 30 15:05:50 2014
New Revision: 22892
URL: http://svn.gna.org/viewcvs/relax?rev=22892&view=rev
Log:
Modified the relax_disp.sherekhan_input to accept dir as input.
bug #21995: (https://gna.org/bugs/index.php?21995) Creating sherekhan input
files, with data for several fields and different time_T2
Modified:
trunk/specific_analyses/relax_disp/sherekhan.py
trunk/user_functions/relax_disp.py
Modified: trunk/specific_analyses/relax_disp/sherekhan.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/sherekhan.py?rev=22892&r1=22891&r2=22892&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/sherekhan.py (original)
+++ trunk/specific_analyses/relax_disp/sherekhan.py Wed Apr 30 15:05:50
2014
@@ -26,26 +26,29 @@
import dep_check
# Python module imports.
+from os import sep
PIPE, Popen = None, None
if dep_check.subprocess_module:
from subprocess import PIPE, Popen
# relax module imports.
from lib.errors import RelaxError, RelaxNoSequenceError
-from lib.io import open_write_file
+from lib.io import mkdir_nofail, open_write_file
from lib.physical_constants import g1H, g15N
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data,
return_residue
from specific_analyses.relax_disp.data import loop_cluster, loop_exp_frq,
loop_offset_point, return_param_key_from_data, spin_ids_to_containers
-def sherekhan_input(spin_id=None, force=False):
+def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'):
"""Create the ShereKhan input files.
@keyword spin_id: The spin ID string to restrict the file
creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all
pre-existing files to be overwritten.
@type force: bool
+ @keyword dir: The optional directory to place the files
into. If None, then the files will be placed into the current directory.
+ @type dir: str or None
"""
# Test if the current pipe exists.
@@ -63,6 +66,10 @@
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been
specified.")
+ # Directory creation.
+ if dir != None:
+ mkdir_nofail(dir, verbosity=0)
+
# Loop over the spin blocks.
cluster_index = 0
for spin_ids in loop_cluster():
@@ -73,7 +80,10 @@
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (mi+1)
- dir_name = 'cluster%s' % (cluster_index+1)
+ if dir != None:
+ dir_name = dir + sep + 'cluster%s' % (cluster_index+1)
+ else:
+ dir_name = 'cluster%s' % (cluster_index+1)
file = open_write_file(file_name=file_name, dir=dir_name,
force=force)
# The B0 field for the nuclei of interest in MHz (must be
positive to be accepted by the server).
Modified: trunk/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=22892&r1=22891&r2=22892&view=diff
==============================================================================
--- trunk/user_functions/relax_disp.py (original)
+++ trunk/user_functions/relax_disp.py Wed Apr 30 15:05:50 2014
@@ -949,6 +949,14 @@
desc = "The spin identification string.",
can_be_none = True
)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir sel",
+ desc_short = "directory name",
+ desc = "The directory name to place ShereKhan cluster folders into.",
+ can_be_none = True
+)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This creates the files required for the ShereKhan
server located at http://sherekhan.bionmr.org/. One file per spin cluster
per field strength will be created. These will be placed in the directory
'clusterx' and named 'sherekhan_frqy.in', where x is the cluster index
starting from 1 and y is the magnetic field strength index starting from 1.")
r22892 - in /trunk: specific_analyses/relax_disp/sherekhan.py user_functions/relax_disp.py